Experiments

Rat

..experiment description ..

Human

..experiment description ..

Bioinformatic analysis

Human data analysis

• Differentially expressed genes
• Ontology analysis

CAGE-seq analysis

• GTRD database
• TSS and DEGs
• Key master regulators of co-expressed genes
• Gene set enrichment analysis (GSEA)
• Unique intergenic TSS
• Alternative usage of dominating TSS
• Enhancers
• Merging CAGE experiments
• Methods
• References

Mathematical modelling

Linkage of metabolic pathways and gene expression

• MetGeneConjugation

Pathways and key proteins

• AMPK
• Ca-CaM-AMPK signaling models
• CaMKII
• CaMKKβ
• LKB1

Models

• Muscle models
• DataSets

Integrated modular models

• ...
• Model validation

Publications of the project

• GTRD: a database on gene transcription regulation
• Modular Visual Model of Energy Metabolism in Human Skeletal Muscle
• A mathematical model linking signalling pathway and gene expression regulation in Human Skeletal Muscle
• Integrated Modular Model Linking Metabolism, Signaling Transduction and Gene Expression Regulation in Human Skeletal Muscle.
• Regulation of Proteins in Human Skeletal Muscle: The Role of Transcription
• Transcriptomic Signatures and Upstream Regulation in Human Skeletal Muscle Adapted to Disuse and Aerobic Exercise
• Genome-wide atlas of promoters expression reveals contribution of transcribed regulatory elements to genetic control of disuse-mediated atrophy, under review